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Orangepipeline merged - #96

Merged

Vghxv merged 132 commits into

masterfrom

orangepipeline-merged

Oct 17, 2026

Merged

Orangepipeline merged#96
Vghxv merged 132 commits into
masterfrom
orangepipeline-merged

Commits on Nov 30, 2024
- [add] re-split lung datasets
  Vghxv
  committed
  101c99e
- [add] preprocessing 📩
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  committed
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- [add] add terms count and dbeta TSS data files for lung tissue analysis
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  26b477b
- [add] add toml package dependency and update poetry.lock
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Commits on Dec 2, 2024
- [add] add plotly and nbformat package dependencies
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- add new analysis scripts for lung tissue data processing
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- add configuration file for lung tissue analysis preprocessing parameters
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Commits on Dec 4, 2024
- add google authentication package dependencies
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- add .gitignore entries for pickle files and credentials
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- add utility functions for Google Drive authentication and file uploads
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- [update] result updates
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- add global CONFIG_PATH variable to store configuration path
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- add gdown and related dependencies for Google Drive file downloads
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- add error handling for Google Drive file operations
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- add configuration files for prostate, rectal, and stomach tissue data; remove cancer_type from lung configuration
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Commits on Dec 11, 2024
- [add] rectal GDC tissue 450K dbeta
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- [add] rectal GDC tissue 450K filtering by TSS and threshold
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- [update] rectal GDC tissue 450K dbeta and filtering by TSS and threshold
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Commits on Dec 12, 2024
- [add] prostate Orange Pipeline
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  committed
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Commits on Dec 14, 2024
- [update] adjust training and testing sample sizes and class distributions for stomach, rectal, and lung configurations
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  committed
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Commits on Dec 15, 2024
- rewrite RFE
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  committed
  6f0252b
- [add] add FPR, TPR, and results CSV files for lung tissue model evaluations
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  committed
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Commits on Dec 16, 2024
- update RFE
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  committed
  937c52d
- [update] adjust training and testing sample sizes and class distributions for lung, rectal, and stomach configurations
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  committed
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Commits on Dec 17, 2024
- improve function clearity, fix typos
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  committed
  7a57d7a
- [update] lung with oversampling results
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  committed
  8e57de1
Commits on Dec 22, 2024
- fix dbeta calculation
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  committed
  5d6b4bf
- [update] adjust lung configuration parameters for preprocessing and class distribution
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  committed
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- [update] update selected feature names for lung tissue models
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Commits on Dec 23, 2024
Commits on Dec 24, 2024
- [update] ROC curve on testing
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  committed
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Commits on Jan 4, 2025
- update: handle division by zero in specificity calculation with warning message
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  committed
  881e316
- fix: correct spelling of 'specificity' in record function
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  committed
  391d58b
- feat: add ROC curve and performance difference plotting functions
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  committed
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- delete outdated results
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- feat: enhance hierarchical clustering functions to save plots and accept output paths
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- lung no oversample metrics and results
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- feat: stucked
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Commits on Jan 5, 2025
- remove garbge
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- feat: enhance function signatures with type hints and improve performance charting
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- feat: add performance metrics and selected features for lung tissue models
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- general pipeline
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Commits on Jan 6, 2025
- combination
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- feat: add consensus selected features for lung tissue models, clean up
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Commits on Jan 12, 2025
- feat: remove
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Commits on Jan 13, 2025
- prostate ml
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- add ipynb
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  committed
  86b5eda
- prostate clustering
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- fix: update type hints for hierarchical_clustering_compare function
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  committed
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- feat: modules
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- rfe
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- feat: rfe seleted feature names
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Commits on Jan 14, 2025
- update modules
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  committed
  4318832
- feat: sfs pipeline
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- sfs results
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- ignore log
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Commits on Jan 15, 2025
- feat: update selected feature names and add voting metrics
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  committed
  b5ee87f
Commits on Jan 17, 2025
- feat: selected gene cleaning
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  committed
  d95f425
- fix naming
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  committed
  5fe2118
Commits on Jan 18, 2025
- feat: add training parameters for machine learning models
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  committed
  b586fa3
- fix: create logs dir
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  committed
  930adb1
- fix confusion
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  c444856
- fix stupid logic
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  3240377
Commits on Feb 2, 2025
- Merge branch 'lung' into prostate
  pizza6inch
  committed
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Commits on Feb 3, 2025
- testing
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- workflow done
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- new rfe sfs results
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Commits on Feb 6, 2025
- lung results
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- final polish
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  e41903b
- remove old files
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  2fc0dcd
- add cat
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  a712d22
- update lock file
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- Revert "update lock file"
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  committed
  834c69a
- refactor configuration and notebook to streamline data file references
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  committed
  37ed86b
- remove unused function to clean up dataset processing code
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  committed
  0651ec0
- add README.md for configuration details and data processing parameters
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Commits on Feb 7, 2025
- Merge branch 'lung' into prostate
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  committed
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Commits on Feb 8, 2025
- [RFE] select2-6 & select 1-5
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  committed
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- [RFE] select 1-5
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  committed
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- [add] result before sfs(section 3)
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- [update] result before sfs(section 3)
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Commits on Feb 9, 2025
- GDC_prostate_tissue pipeline result
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  committed
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- delete previous result
  pizza6inch
  committed
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- GSE269244 result
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- [add] selected features using SFS and RFE
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- [add] section 6
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- [add] section 6 (SFS result)
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Commits on Feb 10, 2025
- GDC with oversample
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  committed
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Commits on Feb 14, 2025
- rfe 1-5 planA
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  committed
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Commits on Feb 15, 2025
- [update] best combination result using GDC
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  committed
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- [add] Plan A stop (while selecting best comb)
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Commits on Feb 16, 2025
- sfs planA
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  committed
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- sfs planA (toml)
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  committed
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- rfe 1-5 planA
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  committed
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- config
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  committed
  ad750a7
- sfs planA
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  committed
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Commits on Feb 17, 2025
- rfe1-5 planA
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  committed
  02d8bd0
- sfs & simpleModel training
  pizza6inch
  committed
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- rfe1-5 planA tmp
  OuChiaYun
  committed
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- [update] Plan A
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- some cool updates with plan A
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Commits on Feb 18, 2025
- typo
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  b5fabe1
- SFS planA
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  committed
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Commits on Feb 19, 2025
- Merge branch 'lung' into prostate/GSE269244
  pizza6inch
  committed
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- toml settings
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  committed
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- Merge remote-tracking branch 'origin/lung' into breast-orangepipline
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- RFE - other planA result(TCGA GEO)
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- Merge remote-tracking branch 'origin/lung' into stomach-orangepipline
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- save combine result
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- RFE other planA
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Commits on Feb 20, 2025
- plan_A_section 2
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- renaming folders
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- some updates
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Commits on Feb 22, 2025
- set the index of the last row as "label" in split_dataset function
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Commits on Feb 23, 2025
- [add] Orange-pipeline plan A result (SMOTE oversample)
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Commits on Oct 17, 2026
- [update] champ env
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  cc03af8
- [revert] restore orchestrator notebook to lung base version
  
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- [revert] restore orchestrator notebook to lung base version
  
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  e694693
- [rename] add _oversample suffix to files conflicting with GSE269244
  
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  claude
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  3d87258
- [remove] accidentally committed config/breast.toml
  
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  claude
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- Merge branch 'rectal-orangepipline' into orangepipeline-merged
  
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- Merge branch 'stomach-orangepipline' into orangepipeline-merged
  
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- Merge branch 'breast-orangepipline' into orangepipeline-merged
  
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- Merge branch 'prostate/GSE269244' into orangepipeline-merged
  
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- Merge branch 'prostate/GDC_prostate_tissue' into orangepipeline-merged
  
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- Merge branch 'rectal_plan_A_results_SMOTE' into orangepipeline-merged
  
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- Merge branch 'clean_up' into orangepipeline-merged
  
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  claude
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- Update r-utils-check workflow to enhance caching and upgrade checkout action
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- Enhance r-utils-check workflow by adding environment variables for test packages and improving renv caching mechanism
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  ecbf2ba

Commits

Commits on Nov 30, 2024

Commits on Dec 2, 2024

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Commits on Dec 11, 2024

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Commits on Jan 4, 2025

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Commits on Jan 6, 2025

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Commits on Jan 15, 2025

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Commits on Feb 19, 2025